Re: [Freesurfer] Demeaning variables

On 11/29/16 8:52 PM, Rodrigo Gonzalez Huerta wrote: It makes sense to me, I only have two more questions, 1. When you say “see if there are any places where there is an interaction between age and group”, do you mean finding significant statistical regions, right? And this would be b

Re: [Freesurfer] Demeaning variables

It makes sense to me, I only have two more questions, 1. When you say “see if there are any places where there is an interaction between age and group”, do you mean finding significant statistical regions, right? And this would be before or after using monte carlo? 2. What about using the

Re: [Freesurfer] Demeaning variables

It comes down to the contrast you care about. If you want to look at the difference in mean thickness between the groups regressing out the effect of age, then demeaning can make a big difference. If this is what you want, then you need to do the analysis in two stages. First run with DODS and

Re: [Freesurfer] Demeaning variables

Hi Doug, I mean that when I run QDEC selecting gender and diagnosis as fixed factors, age as nuisance factor, and display the results, I obtain totally different significant statistical regions (different statistical maps) when ages are demeaned ((demeaned age = age of each subject – the mean

Re: [Freesurfer] recon-all -autorecon2 error.

Hello Doug and Bruce, I ran the script and it worked however, volumes did not align on freeview.* Here's the mri_info for orig.mgz: * Volume information for orig.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1.00, 1.00, 1.00 type: UCHAR (0)

Re: [Freesurfer] ERROR: cannot find RB_all_2008-03-26.gca & Now DYLD Variables

It is not recognizing that the input is a dicom file. Is 4355-0005-1 a dicom file? Or is it a folder? On 11/29/2016 05:51 PM, Douglas Merkitch wrote: > Here is the command/output with the -debug flag: > > recon-all -debug -i > /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reorde

Re: [Freesurfer] ERROR: cannot find RB_all_2008-03-26.gca & Now DYLD Variables

Can you run it with -debug and send the terminal output? On 11/29/2016 05:39 PM, Douglas Merkitch wrote: > Hello Bruce & Doug, > > There are no spaces in the filenames (just a lot of underscores and > dashes!). > > I don't think it's a permissions issue because it is able to write the > first o

Re: [Freesurfer] ERROR: cannot find RB_all_2008-03-26.gca & Now DYLD Variables

Hello Bruce & Doug, There are no spaces in the filenames (just a lot of underscores and dashes!). I don't think it's a permissions issue because it is able to write the first of the two files that I input (regardless of which one I feed it first), but fails to write the second file (what would

Re: [Freesurfer] ERROR: cannot find RB_all_2008-03-26.gca & Now DYLD Variables

Do you have write permission into that folder, ie, /Volumes/Macintosh_HD_2/JGG_freesurfer_v6beta/UIC_3T/1039/mri/orig ? Can you run it with -debug as the first argument and send the terminal output? On 11/29/2016 05:00 PM, Douglas Merkitch wrote: > Hello again, > > I did, in fact, encounter ano

Re: [Freesurfer] ERROR: cannot find RB_all_2008-03-26.gca & Now DYLD Variables

Hi Doug do you have any spaces in your filenames? That can cause this kind of thing. It's hard to tell from your email cheers Bruce On Tue, 29 Nov 2016, Douglas Merkitch wrote: Hello again, I did, in fact, encounter another error that resulted in only the first mri/orig/001.mgz and not the

Re: [Freesurfer] ERROR: cannot find RB_all_2008-03-26.gca & Now DYLD Variables

Hello again, I did, in fact, encounter another error that resulted in only the first mri/orig/001.mgz and not the mr/orig/002.mgz file to be written. Below is the command line and terminal output: === recon-all -i /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG

Re: [Freesurfer] ERROR: cannot find RB_all_2008-03-26.gca

Hello, Sorry for the confusion - the problem was that, while I had changed the $FREESURFER_HOME variable in the mac terminal, I still had the older freesurfer version sourced in my .bashrc file. Once I updated that file, the conversion went on without error. Thanks again for the prompt respons

Re: [Freesurfer] ERROR: cannot find RB_all_2008-03-26.gca

Hello Douglas, Any chance you can upload the two data files 005-SAG_FSPGR_BRAVO_PURE/4355-0005-1 and 4355-0006-1: https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange Ide like to try and reproduce this. Thanks. -Zeke On 11/29/2016 04:20 PM, Douglas Merkitch wrote: > Hello D

Re: [Freesurfer] ERROR: cannot find RB_all_2008-03-26.gca

can you send your command line and full terminal output? On 11/29/2016 04:10 PM, Douglas Merkitch wrote: > Hello experts, > > I was attempting to test out the freesurfer v6 beta and encountered > the following error during dicom conversion: "ERROR: cannot find > /Applications/freesurfer_v6beta_

Re: [Freesurfer] Demeaning variables

When you say that the results are different, what do you mean? What is your contrast? What is your command line? What is your fsgd file? On 11/29/2016 03:34 PM, Rodrigo Gonzalez Huerta wrote: > > Just to clarify, where is said N=18 I wanted to meant 18 controls + 18 > patients. Thanks in advanc

Re: [Freesurfer] TRACULA Error in virtualbox

Hi Alex, Try setting the FSLDIR to when same value as FSL_DIR. So you command would be something like: export FSLDIR=$FSLDIR Then try rerunning TRACULA. Hopefully this solves the issue. -Zeke On 11/29/2016 01:53 PM, Yendiki, Anastasia wrote: > Hi Alex - Have you run the freesurfer setup sc

Re: [Freesurfer] ERROR: cannot find RB_all_2008-03-26.gca

Hello Doug, Command line & terminal output: recon-all -i /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/005-SAG_FSPGR_BRAVO_PURE/4355-0005-1 -i /Volumes/JGG_WD_4TB_hard_drive_2/raw_data_UIC_3T/1039/raw_reordered/006-SAG_FSPGR_BRAVO_PURE_REPEAT/4355-0006-1 -s 1039

[Freesurfer] ERROR: cannot find RB_all_2008-03-26.gca

Hello experts, I was attempting to test out the freesurfer v6 beta and encountered the following error during dicom conversion: "ERROR: cannot find /Applications/freesurfer_v6beta_16Nov2016/average/RB_all_2008-03-26.gca". I'm currently running freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037e

Re: [Freesurfer] Demeaning variables

Just to clarify, where is said N=18 I wanted to meant 18 controls + 18 patients. Thanks in advance. Rodrigo De: freesurfer-boun...@nmr.mgh.harvard.edu en nombre de Rodrigo Gonzalez Huerta Enviado: martes, 29 de noviembre de 2016 02:19:26 p. m. Para: freesurf

[Freesurfer] Demeaning variables

Hi Freesurfers, For obtaining my undergraduate degree I'm performing a study using Freesurfer. I'm stuck with the centering (de-meaning) issue. I have two discrete variables, gender, and patient-control, and a continuous variable which is age. The age population range goes from 20 to 55 years a

Re: [Freesurfer] Using mri_glmfit to generate R (correlation) maps

Ok - no problem. I’ll run again without -wls. Thanks! Keji --- Morenikeji Adebayo Junior Research Fellow Department of Psychiatric Neuroscience Massachusetts General Hospital (p) 617.643.6347 k...@nmr.mgh.harvard.edu > On Nov 29, 2016, at 2:52 PM, Douglas N Gre

Re: [Freesurfer] Using mri_glmfit to generate R (correlation) maps

The pcc calculation is turned off with --wls. I can't remember why I did it that way. On 11/29/2016 02:50 PM, Morenikeji Adebayo wrote: > Hi, > > I’m not sure if this is what you’re looking for but this is the > command I ran: > > /autofs/space/fatfriar_002/cluster/iaslab/NMASA/mri/func/encodin

Re: [Freesurfer] Using mri_glmfit to generate R (correlation) maps

Hi, I’m not sure if this is what you’re looking for but this is the command I ran: /autofs/space/fatfriar_002/cluster/iaslab/NMASA/mri/func/encoding/adebayo/mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --fsgd /autofs/space/fatfriar_001/cluster/iaslab/NMASA/mri/func/encoding/adebayo/allVfix/fsg

Re: [Freesurfer] recon-all -autorecon2 error.

yes, though you should not need to spec the output orientation (redundant) or the in_type (it can figure that out) On 11/29/2016 01:46 PM, miracle ozzoude wrote: > Thanks bruce and doug. The orientation is wrong hence, why I am using > the orientation string. But, the above script is correct? >

Re: [Freesurfer] TRACULA Error in virtualbox

Hi Alex - Have you run the freesurfer setup script? https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall#Setup.26Configuration a.y From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Alexander Zent [az...@p

Re: [Freesurfer] recon-all -autorecon2 error.

Thanks bruce and doug. The orientation is wrong hence, why I am using the orientation string. But, the above script is correct? On Tue, Nov 29, 2016 at 1:39 PM, Douglas N Greve wrote: > don't use the orientation strings unless the orientation is wrong > > > On 11/29/2016 01:38 PM, Bruce Fischl w

Re: [Freesurfer] Using mri_glmfit to generate R (correlation) maps

what is your command line and terminal output? On 11/29/2016 01:24 PM, Morenikeji Adebayo wrote: > Hi there, > > The new mri_glmfit script that I was directed to doesn’t create a file > called “pcc.mgh.” It does create a file called “z.nii.gz” (as far as > I can tell this file is the only diff

Re: [Freesurfer] recon-all -autorecon2 error.

don't use the orientation strings unless the orientation is wrong On 11/29/2016 01:38 PM, Bruce Fischl wrote: > you may not need the out_orientation, but perhaps someone else knows? > On Tue, 29 Nov 2016, miracle ozzoude wrote: > >> Hello Bruce, >> I wanted to confirm if this is the right script

Re: [Freesurfer] recon-all -autorecon2 error.

you may not need the out_orientation, but perhaps someone else knows? On Tue, 29 Nov 2016, miracle ozzoude wrote: Hello Bruce,  I wanted to confirm if this is the right script when converting from one format to another using mri_convert (if i want to use orig.mgz as template volume): mri_conv

Re: [Freesurfer] Using mri_glmfit to generate R (correlation) maps

Hi there, The new mri_glmfit script that I was directed to doesn’t create a file called “pcc.mgh.” It does create a file called “z.nii.gz” (as far as I can tell this file is the only difference between the old and new mri_glm fit scripts). Is there another script that I should be using to gene

Re: [Freesurfer] recon-all -autorecon2 error.

Hello Bruce, I wanted to confirm if this is the right script when converting from one format to another using mri_convert (if i want to use orig.mgz as template volume): mri_convert --in_type analyze --in_orientation LAS -rl orig.mgz --out_type mgz --out_orientation LAS brainmask.img brainmask.mgz

[Freesurfer] Request for patch for mri_convert, nifti1Read(): unsupported slice timing pattern 5 error

Hello Freesurfer experts, I'm trying to run the TRACULA preprocessing pipeline using data in NIFTI-1 format, but am receiving the following error: "nifti1Read(): unsupported slice timing pattern 5" Several other users have run into this problem. In the archives, there are a few links to dead fil